Subsystem: Dihydroxyacetone kinases

This subsystem's description is:

Dihydroxyacetone (DHA) kinases are a sequence-conserved family of enzymes, which utilize two different phosphoryl donors: ATP in animals, plants, and some bacteria, and a phosphocarrier protein HPr of the phosphoenolpyruvate carbohydrate phosphotransferase system (PTS) in most bacteria. ATP- and PTS-dependent DHA kinases display a strikingly high degree of sequence and structure similarity. However, ATP-dependent kinases are generally two-domain proteins, while PTS-dependent kinases are hetero-oligomeric complexes. Both types of DHA kinase invariably contain two subunits/domains: the DhaK subunit/domain covalently binds dihydroxyacetone, while DhaL contains the nucleotide-binding site. In the ATP-dependent kinase, ATP/ADP exchange is fast. In the PTS-dependent kinase, however, ADP is essentially irreversibly bound to DhaL (DhaL-ADP). Here, ADP serves as a cofactor, which is in situ rephosphorylated by a phosphoprotein of the PTS. The PTS-dependent kinases contain an additional subunit, DhaM. In E. coli DhaM consists of three domains, which are homologous to the PTS proteins enzyme I (EI), HPr, and the IIA domain of the PTS transporter for mannose of E. coli. The three domains conduct phosphoryl groups from the general phosphorylcarrier protein HPr of the PTS to the DhaL-ADP complex (Gutknecht et al., 2001). In other organisms the length of a DhaM subunit can vary greatly, reflecting the presence of (i) only IIA domain, (ii) IIA and HPr domains; or of all three domains (as in the E. coli DhaM). DhaM serves as the shuttle for the transfer of phosphate from the bacterial PEP: carbohydrate phosphotransferase system (PTS) to the Dha kinase.

A very high degree of sequence and structure similarity between the two types of DHA kinases, makes it impossible to distinguish the two based on sequence data alone. Hence, the presence/absence of a dhaM homolog in the immediate vicinity of the dhaK and dhaL genes (almost invariably clustered) was used to discern them. Fusion of the two domains into a single DhaK-DhaL polypeptide, characteristic of the ATP-dependent DHA kinases was considered another indicator. However, in several organisms (var. code 2.2) two unfused polypeptides DhaK and DhaL without recognizable DhaM subunits in the same loci were detected. Their specificity is not clear, they are temporarily annotated as “putative ATP-dependent DHA kinases” (even though general Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC and Phosphocarrier protein H can be detected elsewhere in these genomes, e.g. fig|272843.1.peg.897: Pasteurella multocida)


1. Paulsen IT, Reizer J, Jin RZ, Sair MH, Jr. 2000 Functional genomic studies of dihydroxyacetone utilization in Escherichia coli. Microbiology 146:2343-44.
2. Gutknecht R, Beutler R, Garcia-Alles LF, Baumann U, Erni B. 2001. The dihydroxyacetone kinase of Escherichia coli utilizes a phosphoprotein instead of ATP as phosphoryl donor. EMBO J., 20(10):2480-6.
3. Garcia-Alles LF, Siebold C, Nyffeler TL, Flukiger-Bruhwiler K, Schneider P, Burgi HB, Baumann U, Erni B. 2004. Phosphoenolpyruvate- and ATP-dependent dihydroxyacetone kinases: covalent substrate-binding and kinetic mechanism. Biochemistry, 43(41):13037-45.
4. Sun J, van den Heuvel J, Soucaille P, Qu Y, Zeng AP. 2003. Comparative genomic analysis of dha regulon and related genes for anaerobic glycerol metabolism in bacteria. Biotechnol Prog., 19(2):263-72.

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